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comparison tRNAscan.xml @ 0:d34f31cbc9dd draft

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author bgruening
date Sat, 06 Jul 2013 10:37:13 -0400
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1 <tool id="trnascan" name="tRNA prediction" version="0.3">
2 <description>(tRNAscan)</description>
3 <requirements>
4 <requirement type="package" version="1.3.1">tRNAscan-SE</requirement>
5 <requirement type="package" version="1.61">biopython</requirement>
6 </requirements>
7 <command interpreter="python">
8 tRNAscan.py
9 $organism
10 $mode
11 $showPrimSecondOpt
12 $disablePseudo
13 $showCodons
14 -o
15 $tabular_output
16 $inputfile
17 $fasta_output
18 </command>
19 <inputs>
20 <param name="inputfile" type="data" format="fasta" label="Genome Sequence" help="Dataset missing? See TIP below"/>
21 <param name="organism" type="select" label="Select Organism">
22 <option value="">Eukaryotic</option>
23 <option value="-G">general tRNA model</option>
24 <option value="-B">Bacterial</option>
25 <option value="-A">Archaeal</option>
26 <option value="-O">Mitochondrial/Chloroplast</option>
27 </param>
28 <param name="mode" type="select" label="Select Mode">
29 <option value="">Default</option>
30 <option value="-C">Covariance model analysis only (slow)</option>
31 <option value="-T">tRNAscan only</option>
32 <option value="-E">EufindtRNA only</option>
33 <option value="--infernal">Infernal cm analysis (max sensitivity, very slow)</option>
34 <option value="--newscan">Infernal and new cm models</option>
35 </param>
36 <param name="disablePseudo" type="boolean" label="Disable pseudogene checking" truevalue="-D" falsevalue="" />
37 <param name="showPrimSecondOpt" type="boolean" label="Show primary and secondary structure components to Cove scores" truevalue="-H" falsevalue="" />
38 <param name="showCodons" type="boolean" label="Show codons instead of tRNA anticodons" truevalue="-N" falsevalue="" />
39 </inputs>
40 <outputs>
41 <data format="tabular" name="tabular_output" label="${tool.name} on ${on_string}: tabular" />
42 <data format="fasta" name="fasta_output" label="${tool.name} on ${on_string}: fasta" />
43 </outputs>
44 <tests>
45 <test>
46 <param name="input" value="trna_arabidopsis.fasta" ftype="fasta" />
47 <param name="organism" value="" />
48 <param name="mode" value="--infernal" />
49 <param name="disablePseudo" value="" />
50 <param name="showPrimSecondOpt" value="" />
51 <param name="showCodons" value="" />
52 <output name="fasta_output" file="tRNAscan_eukaryotic_infernal.fasta" ftype="fasta" />
53 <output name="fasta_output" file="tRNAscan_eukaryotic_infernal.tabular" ftype="tabular" />
54 </test>
55 </tests>
56 <help>
57
58
59 .. class:: warningmark
60
61 **TIP** This tool requires *fasta* formated sequences.
62
63 -----
64
65 **What it does**
66
67 tRNAscan-SE_ was designed to make rapid, sensitive searches of genomic
68 sequence feasible using the selectivity of the Cove analysis package.
69 We have optimized search sensitivity with eukaryote cytoplasmic and
70 eubacterial sequences, but it may be applied more broadly with a
71 slight reduction in sensitivity.
72
73 .. _tRNAscan-SE: http://lowelab.ucsc.edu/tRNAscan-SE/
74
75 -----
76
77 **Organism**
78
79 - search for eukaryotic cytoplasmic tRNAs:
80
81 This is the default.
82
83 - use general tRNA model:
84
85 This option selects the general tRNA covariance model that was trained
86 on tRNAs from all three phylogenetic domains (Archaea, Bacteria, and
87 Eukarya). This mode can be used when analyzing a mixed collection of
88 sequences from more than one phylogenetic domain, with only slight
89 loss of sensitivity and selectivity. The original publication
90 describing this program and tRNAscan-SE version 1.0 used this general
91 tRNA model exclusively. If you wish to compare scores to those found
92 in the paper or scans using v1.0, use this option. Use of this option
93 is compatible with all other search mode options described in this
94 section.
95
96 - search for bacterial tRNAs
97
98 This option selects the bacterial covariance model for tRNA analysis,
99 and loosens the search parameters for EufindtRNA to improve detection
100 of bacterial tRNAs. Use of this mode with bacterial sequences
101 will also improve bounds prediction of the 3' end (the terminal CAA
102 triplet).
103
104 - search for archaeal tRNAs
105
106 This option selects an archaeal-specific covariance model for tRNA
107 analysis, as well as slightly loosening the EufindtRNA search
108 cutoffs.
109
110 - search for organellar (mitochondrial/chloroplast) tRNAs
111
112 This parameter bypasses the fast first-pass scanners that are poor at
113 detecting organellar tRNAs and runs Cove analysis only. Since true
114 organellar tRNAs have been found to have Cove scores between 15 and 20
115 bits, the search cutoff is lowered from 20 to 15 bits. Also,
116 pseudogene checking is disabled since it is only applicable to
117 eukaryotic cytoplasmic tRNA pseudogenes. Since Cove-only mode is
118 used, searches will be very slow (see -C option below) relative to the
119 default mode.
120
121 ------
122
123 **Mode**
124
125 - search using Cove analysis only (max sensitivity, slow)
126
127 Directs tRNAscan-SE to analyze sequences using Cove analysis only.
128 This option allows a slightly more sensitive search than the default
129 tRNAscan + EufindtRNA -> Cove mode, but is much slower (by approx. 250
130 to 3,000 fold). Output format and other program defaults are
131 otherwise identical to the normal analysis.
132
133 - search using Eukaryotic tRNA finder (EufindtRNA) only:
134
135 This option runs EufindtRNA alone to search for tRNAs. Since Cove is
136 not being used as a secondary filter to remove false positives, this
137 run mode defaults to "Normal" parameters which more closely
138 approximates the sensitivity and selectivity of the original algorithm
139 describe by Pavesi and colleagues.
140
141 - search using tRNAscan only (defaults to strict search parameters)
142
143 Directs tRNAscan-SE to use only tRNAscan to analyze sequences. This
144 mode will cause tRNAscan to default to using "strict" parameters
145 (similar to tRNAscan version 1.3 operation). This mode of operation
146 is faster (about 3-5 times faster than default mode analysis), but
147 will result in approximately 0.2 to 0.6 false positive tRNAs per Mbp,
148 decreased sensitivity, and less reliable prediction of anticodons,
149 tRNA isotype, and introns.
150
151 - search using Infernal cm analysis only (max sensitivity, very slow)
152
153
154 - search using Infernal and new cm models instead of Cove
155
156
157 -----
158
159 **disable pseudogene checking**
160
161 Manually disable checking tRNAs for poor primary or secondary
162 structure scores often indicative of eukaryotic pseudogenes. This
163 will slightly speed the program and may be necessary for non-eukaryotic
164 sequences that are flagged as possible pseudogenes but are known to be
165 functional tRNAs.
166
167 -----
168
169 **Show both primary and secondary structure score components to covariance model bit scores**
170
171 This option displays the breakdown of the two components of the
172 covariance model bit score. Since tRNA pseudogenes often have one
173 very low component (good secondary structure but poor primary sequence
174 similarity to the tRNA model, or vice versa), this information may be
175 useful in deciding whether a low-scoring tRNA is likely to be a
176 pseudogene. The heuristic pseudogene detection filter uses this
177 information to flag possible pseudogenes -- use this option to see why
178 a hit is marked as a possible pseudogene. The user may wish to
179 examine score breakdowns from known tRNAs in the organism of interest
180 to get a frame of reference.
181
182 -----
183
184 **Show codons instead of tRNA anticodons**
185
186 This option causes tRNAscan-SE to output a tRNA's corresponding codon
187 in place of its anticodon.
188
189 -----
190
191 **Example**
192
193 * input:
194
195 >CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7
196 GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
197 GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
198 TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
199 TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
200 GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
201 ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
202 AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
203 .....
204
205
206 * output:
207
208
209 ======== ====== ===== ====== ==== ========== ====== ====== ========== ==========
210 tRNA Bounds Intron Bonds
211 -------- ------ ---------------- ---- ---------- ---------------- ---------- ----------
212 Name # tRNA Begin End tRNA Anti Codon Begin End Cove Score Hit Origin
213 ======== ====== ===== ====== ==== ========== ====== ====== ========== ==========
214 CELF22B7 1 12619 12738 Leu CAA 12657 12692 55.12 Bo
215 CELF22B7 2 19480 19561 Ser AGA 0 0 66.90 Bo
216 CELF22B7 3 26367 26439 Phe GAA 0 0 73.88 Bo
217 CELF22B7 4 26992 26920 Phe GAA 0 0 73.88 Bo
218 CELF22B7 5 23765 23694 Pro CGG 0 0 60.58 Bo
219 ======== ====== ===== ====== ==== ========== ====== ====== ========== ==========
220
221
222 -------
223
224 **References**
225
226 Todd M. Lowe and Sean R. Eddy
227
228 tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Nucl. Acids Res. (1997) 25(5): 0955-964
229
230 doi:10.1093/nar/25.5.0955
231
232
233 </help>
234 </tool>